10:00a – 11:00p
STORM2
- Helping Guipeng and Ruobo get set up on STORM2.
Cell staining
- prepping cells for hybridizaton.
- last row (4 coverslips) forgot to add last rinse of PBS. Cells dried out. Coverslips tossed.
- cells into formamide, ready for staining.
- Samples to test: D8, D10, E3, E11, F3, G4
- All stained, incubating at 47C, ~7pm
Library / Deep Seq analysis
- Rebuilt Lib2 fasta with indexed headers (Library2idx.fasta)
- Re-running bowtie2 on on indexed Lib2 fasta
- still running at 10pm
Computer
- Cajal has 12 memory slots and 6x 4Gb currently on board. Could add 4×4 Gb more from Monet upgrade.
Coding
- Add ROI analysis to STORMfinder
- To add to Insight, modify .ini file to contain in ‘Image’ field the following lines:
ROI Valid=1
ROI_x0=0
ROI_x1=256
ROI_y0=0
ROI_y1=256 - Sync Monet, Tuck and Cajal Git to use ZhuangLab/storm-analysis git repo as the DaoSTORM location (this will remain updated by hazen).
- test insight ROI on STORMfinder. Seems to work excellent
- Investigating new ROI in DaoSTORM
- successfully integrated ROI specification in STORMfinder / matlab-storm repo.
STORM Analysis
- Box4 went unresponsive during final stages of analysis of G9 data. Several daoSTORM runs failed, possibly corrupted.
- Running G1 data on Monet using new ROI finder.
- synched
STORM imaging
- set up overnight STORM of E10rna stained cells in V marked region.
- V clearly visible in 10x image but not in 100x image.
- hopefully the large cells act as landmarks. Could have tried imaging more beads.
Presentations
- working on slides for meeting with Ting
- tentatively scheduled for Dec 3, 2pm.
To address
- extra F6 data set on STORM2. Is this really F6?! Why would I image F6 on 11/08, I had plenty of F6 before. Check with Bogdan.